Fluorescent carbon dots synthesized by waste wind turbine blade for photocatalytic degradation

Developing novel waste recycling strategies has become a feasible solution to overcome environmental pollution. In this work, a method of using waste wind turbine blade (WTB) as a carbon source to synthesize blue fluorescent carbon dots (B-CDs) by hydrothermal treatment is proposed. B-CDs are spherical and have an average particle size of 5.2 nm. The surface is rich in C–O, C=O, −CH₃, and N–H bond functional groups, containing five elements: C, O, N, Si, and Ca. The optimal emission wavelength of B-CDs is 463 nm, corresponding to an excitation wavelength of 380 nm. Notably, a relatively high quantum yield of 29.9% and a utilization rate of 40% were obtained. In addition, B-CDs can serve as a photocatalyst to degrade methylene blue dye, with a degradation efficiency of 64% under 40-min irradiation conditions. The presence of holes has a significant influence on the degradation process.     

Hypothesis of a proton switch in QM/MM modelling of interaction of dUMP analogues with thymidylate synthase

Quantum mechanical, molecular mechanics and molecular dynamics (MD) methods were used to investigate initial steps of 2′-deoxyuridine-5′-monophosphate (dUMP) methylation catalysed by the thymidylate synthase (TS) enzyme. The amino acid residues surrounding the active site within a 10 Å radius sphere were modelled with the combined quantum mechanical (B3LYP/LANL2DZ) and molecular mechanics ONIOM double-layer method. The results indicated the initial nucleophilic attack of Cys146 on dUMP to be concerted with formation of a hydrogen bond to the oxygen O4 of dUMP. Moreover, the proton in the vicinity of the O4 atom appears to act as a ‘proton switch’: if a proton is present near O4, it stabilises the S(Cys146)–C6(dUMP) sulphur–carbon bond, but if it is absent, the sulphur–carbon bond does not form. If the O4 oxygen is replaced by sulphur atom, the ‘switch effect’ does not occur. The suggested correlation between the strength of hydrogen bond involving O4 oxygen and the ability of dUMP to form bonds at C6 corresponds well to the crystal structures of TS complexes available in the Protein Data Bank. In the vast majority of crystal structures, the presence of the S(Cys146)–C6(dUMP) bond was coupled with the presence of hydrogen bond between the dUMP O4 atom and the conserved Asn177. The ‘proton switch’ hypothesis is supported also by the results of MD studies of TS binary complexes, suggesting that average distance separating S(Cys146) and C6(dUMP) becomes distinctly shorter in the presence of hydrogen bonding between Asn177 and O4.     

Theoretical investigation on the structure and thermodynamic properties of the 2,4-dinitroimidazole complex with methanol

The structure and thermodynamic properties of the 2, 4-dinitroimidazole complex with methanol were investigated using the B3LYP and MP2(full) methods with the 6-31++G(2d,p) and 6-311++G(3df,2p) basis sets. Four types of hydrogen bonds [N–H?O, C–H?O, O–H?O (nitro oxygen) and O–H?π] were found. The hydrogen-bonded complex having the highest binding energy had a N–H?O hydrogen bond. Analyses of natural bond orbital (NBO) and atoms-in-molecules (AIM) revealed the nature of the intermolecular hydrogen-binding interaction. The changes in thermodynamic properties from monomers to complexes with temperatures ranging from 200.0 to 800.0 K were investigated using the statistical thermodynamic method. Hydrogen-bonded complexes of 2,4-dinitroimidazole with methanol are fostered by low temperatures.

Fe–O versus O–O bond cleavage in reactive iron peroxide intermediates of superoxide reductase

It is generally accepted that the catalytic cycles of superoxide reductases (SORs) and cytochromes P450 involve a ferric hydroperoxo intermediate at a mononuclear iron center with a coordination sphere consisting of four equatorial nitrogen ligands and one axial cysteine thiolate trans to the hydroperoxide. However, although SORs and P450s have similar intermediates, SORs selectively cleave the Fe–O bond and liberate peroxide, whereas P450s cleave the O–O bond to yield a high-valent iron center. This difference has attracted the interest of researchers, and is further explored here. Meta hybrid DFT (M06-2X) results for the reactivity of the putative peroxo/hydroperoxo reaction intermediates in the catalytic cycle of SORs were found to indicate a high-spin preference in all cases. An exploration of the energy profiles for Fe–O and O–O bond cleavage in all spin states in both ferric and ferrous models revealed that Fe–O bond cleavage always occurs more easily than O–O bond cleavage. While O–O bond cleavage appears to be thermodynamically and kinetically unfeasible in ferric hydrogen peroxide complexes, it could occur as a minor (significantly disfavored) side reaction in the interaction of ferrous SOR with hydrogen peroxide.     

Pressure dependence on electronic structures,charge distribution and bond orders of solid nitromethane using nonlocal DFT functional

The electronic properties of solid nitromethane are studied using nonlocal exchange-correlation functional (optPBE–vdW) under hydrostatic compression up to 40?GPa. We found that the optPBE–vdW functional can reproduce well the crystalline structures compared with the experiments, and an isomorphic phase transition has been verified by their P–V curve. Bader’s charge analysis shows the electron flows from CH₃ group to NO₂ group with the pressure. Moreover, the calculated bond orders show that the pressure only strengthens the intermolecular C–N bond and intermolecular C–H···O hydrogen bonds though it shortens all bond lengths. Furthermore, the electronic structure and its pressure dependence have also been discussed in detail.     

Theoretical studies on the structures,intra- and inter-molecular hydrogen bonding interactions in HNF and HNF–H2O clusters in the gaseous,aqueous and solid phases

Hydrazimium nitroformate ([N₂H₅]⁺[C(NO₂)₃]^? , HNF) is an ionic oxidiser used in solid propellants. Its properties are easily affected by H₂O because of its hygroscopicity. In this article, density functional theory (DFT) and molecular dynamics (MD) were employed to study the isolated HNF molecule and the HNF–H₂O cluster in gas phase and in the aqueous solution. Three stable conformations were obtained for HNF in the gas phase and in the aqueous solution, respectively, and each conformation can form several different HNF–H₂O clusters. Irrespective of whether it is in gas phase or in solution, intramolecular hydrogen bond interactions and other interactions (e.g. the binding energy, the dispersion energy, the second-order perturbation energy and the energy gap between frontier orbitals) of HNF are weaker in the clusters than in the isolated state. The initial decomposition energy of the cluster is lower than that of the isolated HNF molecule in both gaseous and aqueous phases, while the dissociation processes are the same. Molecular dynamic simulations showed that the clustered H₂O elongates and weakens the C–NO₂ bond in the solid HNF–H₂O cluster compared with that in the solid HNF. H₂O reduces and weakens intramolecular N–HΛO bonds too, and O–HΛN is the dominant intermolecular hydrogen bond between HNF and H₂O.     

Crystal Structure and Conformation of 5‐Fluorouridine: Conformational Preferences for 5‐Fluorinated Pyranosides

Crystals of 5‐fluorouridine (5FUrd) have unit cell dimensions a = 7.716(1), b = 5.861(2), c = 13.041(1)Å, α = γ = 90°, β = 96.70° (1), space group P2₁, Z = 2, ρ_obs = 1.56 gm/c.c and ρ_calc = 1574 gm/c.c The crystal structure was determined with diffractometric data and refined to a final reliability index of 0.042 for the observed 2205 reflections (I ≥ 3σ). The nucleoside has the anti conformation [χ = 53.1(4)°] with the furanose ring in the favorite C2′–endo conformation. The conformation across the sugar exocyclic bond is g⁺, with values of 49.1(4) and ? 69.3(4)° for Φ_θc and Φ_∞ respectively. The pseudorotational amplitude τ_m is 34.5 (2) with a phase angle of 171.6(4)°. The crystal structure is stabilized by a network of N–H…O and O–H…O involving the N3 of the uracil base and the sugar O3′ and O2′ as donors and the O2 and O4 of the uracil base and O3′ oxygen as acceptors respectively. Fluorine is neither involved in the hydrogen bonding nor in the stacking interactions. Our studies of several 5‐fluorinated nucleosides show the following preferred conformational features: 1) the most favored anti conformation for the nucleoside [χ varies from ? 20 to + 60°] 2) an inverse correlation between the glycosyl bond distance and the χ angle 3) a wide variation of conformations of the sugar ranging froni C2′–endo through C3′–endo to C4′–exo 4) the preferred g⁺ across the exocyclic C4′–C5′ bond and 5) no role for the fluorine atom in the hydrogen bonding or base stacking interactions.     

The resonance Raman frequencies of the Fe-CO stretching and bending modes in the CO complex of cytochrome P-450cam

Resonance Raman spectra of the ferrous CO complex of cytochrome P-450cam have been observed both in its camphor-bound and free states. Upon excitation at 457.9 nm, near the absorption maximum of the Soret band, the ferrous CO complex of the camphor-bound enzyme showed an anomalously intense Raman line at 481 cm-1 besides the strong Raman lines at 1366 and 674 cm-1 for the porphyrin vibrations. The Raman line at 481 cm-1 (of the 12C16O complex) shifted to 478 cm-1 upon the substitution by 13C16O and to 473 cm-1 by 12C18O without any detectable shift in porphyrin Raman lines. This shows that the line at 481 cm-1 is assignable to Fe-CO stretching vibration. By the excitation at 457.9 nm, a weak Raman line was also observed at 558 cm-1, which was assigned to the Fe-C-O bending vibration, because it was found to shift by -14 cm-1 on 13C16O substitution while only -3 cm-1 on 12C18O substitution. These stretching and bending vibrations of the Fe-CO bond were not detected with the excitation at 413.1 nm, though the porphyrin Raman lines at 1366 and 674 cm-1 were clearly observed. When the substrate, camphor, was removed from the enzyme, the Fe-CO stretching vibration was found to shift to 464 cm-1 from 481 cm-1, while no detectable changes were found in porphyrin Raman lines. This means that the bound substrate interacts predominantly with the Fe-CO portion of the enzyme molecule.     

Rates of oxygen and hydrogen exchange as indicators of TPQ cofactor orientation in amine oxidases.

This study presents the first detailed examination by resonance Raman (RR) spectroscopy of the rates of solvent exchange for the C5 and C3 positions of the TPQ cofactor in several wild-type copper-containing amine oxidases and mutants of the amine oxidase from Hansenula polymorpha (HPAO). On the basis of crystal structure analysis and differing rates of C5 [double bond] O and C3 [bond] H exchange within the enzyme systems, but equally rapid rates of C5 [double bond] O and C3 [bond] H exchange in a TPQ model compound, it is proposed that these data can be used to determine the TPQ cofactor orientation within the active site of the resting enzyme. A rapid rate of C5 [double bond] O exchange (t(1/2) < 30 min) and a slow (t(1/2) = 6 h) to nonexistent rate of C3 [bond] H exchange was observed for wild-type HPAO, the amine oxidase from Arthrobacter globiformis, pea seedling amine oxidase at pH 7.1, and the E406Q mutant of HPAO. This pattern is ascribed to a productive TPQ orientation, with the C5 [double bond] O near the substrate-binding site and the C3 [bond] H near the Cu. In contrast, a slow rate of C5 [double bond] O exchange (t(1/2) = 1.6-3.3 h) coupled with a fast rate of C3 [bond] H exchange (t(1/2) < 30 min) was observed for the D319E and D319N catalytic base mutants of HPAO and for PSAO at pH 4.6 (t(1/2) = 4.5 h for C5 [double bond] O exchange). This pattern identifies a flipped orientation, involving 180 degrees rotation about the C alpha-C beta bond, which locates the C3 [bond] H near the substrate-binding site and the C5 double bond] O near the Cu. Finally, fast rates of both C5 [double bond] O and C3 [bond] H exchange (t(1/2) < 30 min) were observed for the amine oxidase from Escherichia coli and the N404A mutant of HPAO, suggesting a mobile cofactor, with multiple TPQ orientations between productive and flipped. These results demonstrate that opposing sides of the TPQ ring possess different degrees of solvent accessibility and that the rates of C5 [double bond] O and C3 [bond] H exchange can be used to predict the TPQ cofactor orientation in the resting forms of these enzymes.     

Hydrothermal deposition synthesis of dual-mode luminescent material GdVO4:Eu3+/carbon dots with optimal luminescence and its application in anti-counterfeiting

To obtain optimal luminescence, 0.12 g of GdVO₄:3%Eu³⁺ nanocrystals (NCs) and different volumes of nitrogen-doped carbon dots (N-CDs) crude solution were used as precursors, and the composite synthesized using the hydrothermal deposition method showed optimal luminescence when 11 ml (2.45 mmol) crude solution was used. In addition, similar composites with the same molar ratio as GVE/cCDs(11) were also prepared with the hydrothermal and physical mixing processes. Based on the test results of XRD, XPS, and PL spectra, for the composite GVE/cCDs(11), the highest (lowest) peak intensity of the C–C/C=C (C=O/C=N) bond, which was 1.18 (0.75) times that of GVE/cCDs-m, indicated most N-CDs deposition and led to their highest emission intensity under 365 nm excitation, although nitrogen atoms in the composite were shed slightly during the deposition process. Finally, as can be seen from the patterns designed for security applications that the optimally luminescent composite is one of the most promising candidates in the anti-counterfeiting field.     

Non-empirical valence bond calculation of hydrogen bond energy in polypeptides

An approximate ab-initio valence bond calculation of hydrogen bond energy was carried out and the results are discussed. The total bond energy of a simplified N? H…O structure is calculated for various N? H and N…O distances and the potential energy profiles are obtained. The hydrogen bond energy, ie, the delocalization energy gained by the formation of one hydrogen bond is found to be 8.7–12.0 kcal/mole. The potential energy is characterized by a deep minimum at 1.6–1.8 a.u. from the nitrogen and the second trough is found to be considerably higher than the first.     

Radical formation in pyrimidines. IV. 1,3-dimethyluracil, a non-hydrogen-bonding crystal.

Radical formation in single crystals of 1,3-dimethyluracil by X-irradiation has been studied by electron spin resonance at 9.5 GHz. This crystal contains no hydrogen bonds. Only Van der Waals forces are present. Accordingly, after X-irradiation at 300 K, the only radicals observed are those resulting from the excitation path: the H-addition radical at C5 and an H-abstraction radical from a methyl group. Irradiation with light of lambda more than 400 nm induces the transformation of the C5-addition into the C6-addition radical. INDO calculations indicate that the C6-addition radical is protonated at O4. Since this crystal does not contain N-H or O-H bonds, this protonation can only occur through proton-abstraction from a C-H bond of a neighbouring molecule by the carbonyl group. The presence of short contacts between C6 and O4 is taken to suggest that the abstraction occurs at C6.     

13C‐NMR chemical shift tensor and hydrogen‐bonded structure of glycine‐containing peptides in a single crystal

¹³C‐nmr chemical shift tensor components are reported for a ¹³C‐labeled Gly¹ amide carbonyl carbon of a glycylglycine (Gly¹Gly²) single crystal, a GlyGly · HNO₃ single crystal and a GlyGly · HCl · H₂O single crystal, for which the three‐dimensional crystal structures have already been determined by x‐ray diffraction. The tensor components were measured by changing the angle between the crystal plane and the applied magnetic field by using a goniometer designed in this work for use in conventional ¹³C cross‐polarization/magic angle spinning nmr probe. From these experimental data, the principal values of the ¹³C chemical shift tensor and its directions for the Gly¹ amide carbonyl carbon were determined. It was found that the ¹³C chemical shift tensor components (δ₁₁, δ₂₂, and δ₃₃) for the Gly¹ amide carbonyl carbon in GlyGly and GlyGly · HNO₃ with a >NH · · · OC< type of hydrogen bond depend on the hydrogen‐bond length and the directions of the δ₂₂ components of these peptides are along the hydrogen‐bonded >CO bond axis. In addition, the magnitude of the deviation from the bond axis depends on the hydrogen‐bond angle. Further, the experimental result for GlyGly · HCl · H₂O with a  O H · · ·OC< type of hydrogen bond was discussed. © 1999 John Wiley & Sons, Inc. Biopoly 50: 61–69, 1999     

Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory

Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H(A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H-N3(T), present in A-T base pair is also investigated.      

Charge influence on the first dehydrogenation of methanol by Pt<Subscript>n</Subscript><Superscript>q</Superscript> (<Emphasis Type="Italic">n </Emphasis>= 1–3, q = 0, +1, −1): a computational study

Understanding the bond-cleavage ability of metal clusters is very important in various fields, such as catalysis and surface science. In this work, we performed density functional theory calculations on the first dehydrogenation process (also the key step) of methanol on Pt_n ^q (n = 1–3, q = 0, +1, ?1) clusters in varied charge states using quantum chemical calculations. It is shown that methanol is adsorbed much more easily to the cationic Pt_n ⁺ than to the neutral and anionic Pt_n ^0/?. By contrast, the intrinsic bond cleavage barriers of both C–H and O–H on the cationic Pt_n ⁺ are significantly higher than on Pt_n ^0/? (the only exception is the C–H bond cleavage on Pt⁺). Promisingly, injecting an electron to the neutral Pt_n ⁰ to give Pt_n ^? can greatly reduce the C–H/O–H bond scission barrier while maintaining appreciable adsorption energy. The charging effect can be nicely interpreted by the nature of the frontier orbitals of Pt_n ^q.     

Approaches to the simultaneous inactivation of metallo- and serine-β-lactamases

A series of cephalosporin-derived reverse hydroxamates and oximes were prepared and evaluated as inhibitors of representative metallo- and serine-β-lactamases. The reverse hydroxamates showed submicromolar inhibition of the GIM-1 metallo-β-lactamase. With respect to interactions with the classes A, C, and D serine β-lactamases, as judged by their correspondingly low K_m values, the reverse hydroxamates were recognized in a manner similar to the non-hydroxylated N–H amide side chains of the natural substrates of these enzymes. This indicates that, with respect to recognition in the active site of the serine β-lactamases, the OC–NR–OH functionality can function as a structural isostere of the OC–NR–H group, with the N–O–H group presumably replacing the amide N–H group as a hydrogen bond donor to the appropriate backbone carbonyl oxygen of the protein. The reverse hydroxamates, however, displayed k_cat values up to three orders of magnitude lower than the natural substrates, thus indicating substantial slowing of the hydrolytic action of these serine β-lactamases. Although the degree of inactivation is not yet enough to be clinically useful, these initial results are promising. The substitution of the amide N–H bond by N–OH may represent a useful strategy for the inhibition of other serine hydrolases.     

31P NMR and Computational Studies on Stereochemistry of Conversion of Phosphoramidate Diesters into the Corresponding Phosphotriesters

³¹P NMR spectroscopy was used to investigate a stereochemical course of a nitrite-promoted conversion of phosphoramidate diesters into the corresponding phosphotriesters. It was found that this reaction occurred with almost complete epimerization at the phosphorus center and at the C1 atom in the amine moiety. On the basis of the ³¹P NMR data, a plausible mechanism for the reaction was proposed. The density functional theory calculation of the key step of the reaction, i.e., breaking of the P–N bond and formation of the P–O bond, suggested a one-step S_N2(P) process with retention of configuration at the phosphorus center.     

C‐H…O hydrogen bonds in FK506‐binding protein–ligand interactions

Hydrogen bonds are important interaction forces observed in protein structures. They can be classified as stronger or weaker depending on their energy, thereby reflecting on the type of donor. The contribution of weak hydrogen bonds is deemed as an important factor toward structure stability along with the stronger bonds. One such bond, the C‐H…O type hydrogen bond, is shown to make a contribution in maintaining three dimensional structures of proteins. Apart from their presence within protein structures, the role of these bonds in protein–ligand interactions is also noteworthy. In this study, we present a statistical analysis on the presence of C‐H…O hydrogen bonds observed between FKBPs and their cognate ligands. The FK506‐binding proteins (FKBPs) carry peptidyl cis–trans isomerase activity apart from the immunosuppressive property by binding to the immunosuppressive drugs FK506 or rapamycin. Because the active site of FKBPs is lined up by many hydrophobic residues, we speculated that the prevalence of C‐H…O hydrogen bonds will be considerable. In a total of 25 structures analyzed, a higher frequency of C‐H…O hydrogen bonds is observed in comparison with the stronger hydrogen bonds. These C‐H…O hydrogen bonds are dominated by a highly conserved donor, the C^α/β of Val55 and an acceptor, the backbone oxygen of Glu54. Both these residues are positioned in the β4‐α1 loop, whereas the other residues Tyr26, Phe36 and Phe99 with higher frequencies are lined up at the opposite face of the active site. These preferences could be implicated in FKBP pharmacophore models toward enhancing the ligand affinity. This study could be a prelude to studying other proteins with hydrophobic pockets to gain better insights into ligand recognition. Copyright © 2013 John Wiley & Sons, Ltd.     

Model systems for flavoenzyme activity. The effects of specific hydrogen bonds on the 13C and 1H NMR of flavins

We have developed a family of receptors designed to bind flavin derivatives using specific hydrogen bond interactions. These synthetic host molecules provide a model for specific flavoenzyme–cofactor interactions, allowing isolation and observation of the effects of hydrogen bonding on flavin NMR. We describe here the use of one of these receptors to study the effects of hydrogen bonding to O(2), N(3), and O(4) on flavin ¹H and ¹³C NMR.     

Mn‐Rich P′2‐Na0.67[Ni0.1Fe0.1Mn0.8]O2 as High‐Energy‐Density and Long‐Life Cathode Material for Sodium‐Ion Batteries

Herein, P′2‐type Na_0.67[Ni_0.1Fe_0.1Mn_0.8]O₂ is introduced as a promising new cathode material for sodium‐ion batteries (SIBs) that exhibits remarkable structural stability during repetitive Na⁺ de/intercalation. The O? Ni? O? Mn? O? Fe? O bond in the octahedra of transition‐metal layers is used to suppress the elongation of the Mn? O bond and to improve the electrochemical activity, leading to the highly reversible Na storage mechanism. A high discharge capacity of ≈220 mAh g^?1 (≈605 Wh kg^?1) is delivered at 0.05 C (13 mAg^?1) with a high reversible capacity of ≈140 mAh g^?1 at 3 C and excellent capacity retention of 80% over 200 cycles. This performance is associated with the reversible P′2–OP4 phase transition and small volume change upon charge and discharge (≈3%). The nature of the sodium storage mechanism in a full cell paired with a hard carbon anode reveals an unexpectedly high energy density of ≈542 Wh kg^?1 at 0.2 C and good capacity retention of ≈81% for 500 cycles at 1 C (260 mAg^?1).